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Sample GSM219172 Query DataSets for GSM219172
Status Public on Aug 20, 2007
Title Whole BF 48H rep3
Sample type RNA
 
Source name Whole mosquito 48 hours post-bloodmeal
Organism Anopheles gambiae
Characteristics Strain:pink-eye
Treatment protocol Animals were maintained at 25°C, 75–85% relative humidity and a 18/6 h light/dark cycle.
Growth protocol Larvae were fed on finely powdered fish food (Tetramind, Tetra Werke, Germany) mixed 1:1 with yeast powder. Adults (males and females) were kept in cages with access ad libitum to raisins and water. For blood feeding, adult female mosquitoes were fed on mice anaesthetized with a mixture of ketamine and xylazine. Males and females were kept together in the cage until the blood meal. Blood-fed females were transferred to a separate cage and kept without males for the remaining duration of the experiment. The transferred females were kept with access to raisins and water and were offered a cup with water as oviposition site at all times. Egg laying was observed between 72 and 96 h PBM. Three samples composed of five mosquitoes each were collected for each experimental time point, the RNA was immediately extracted and stored at -80°C.
Extracted molecule total RNA
Extraction protocol Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD, USA) and purified further by passing it through an RNeasy spin column (Qiagen, Chatsworth, CA, USA). Eluted total RNAs were quantified and a portion of the recovered material adjusted to a final concentration of 1 µg/µl. All starting total RNA samples were quality-assessed prior to beginning target preparation/processing steps by resolving a small amount of each sample (typically 25–250 ng/well) on to a RNA Laboratory-On-A-Chip (Caliper Technologies, Mountain View, CA, USA) that was evaluated on an Agilent Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA, USA).
Label biotin
Label protocol Single-stranded, then double-stranded cDNA was synthesized from the poly (A)+ mRNA present in the isolated total RNA (10 µg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA, USA) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds-cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA). 15 µg of the resulting biotin-tagged cRNA were fragmented to strands of 35–200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
 
Hybridization protocol 10 µg of this fragmented target cRNA was hybridized at 45 °C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip® Plasmodium/Anopheles Genome Array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
Scan protocol Scanning was performed on a GeneChip Scanner 3000. The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.).
Description A searchable database (Anopheles gambiae Gene Expression Database at UC Irvine) has been made available so that detailed analyses of specific groups of genes based on their descriptions, functions or levels of gene expression variation can be performed. Related publications: Dissanayake, S., Marinotti, O., Ribeiro, J.M.C., & James, A.A. (2006) angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences. BMC Genomics 7:116. & Marinotti, O., Calvo, E., Nguyen, Q. K., Dissanayake, S., Ribeiro, J. M. C., & James, A. A. (2006) Genome-wide analysis of gene expression in adult Anopheles gambiae. Insect Mol Biol 15 (1), 1-12. Marinotti, O., Nguyen, Q. K., Calvo, E., James, A. A., & Ribeiro, J. M. C. (2005) Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae. Insect Mol Biol 14 (4), 365-373.
Data processing The results were quantified and analysed using GCOS software (version 1.1.1, Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values).
 
Submission date Aug 20, 2007
Last update date Aug 14, 2011
Contact name Osvaldo Marinotti
E-mail(s) angaged@gmail.com
Organization name University of California, Irvine
Department Molecular Biology & Biochemistry
Lab Anthony James
Street address University of California, Irvine
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL1321
Series (1)
GSE8822 Anopheles gambiae genome-wide gene expression in response to bloodmeal

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 444.129 P 0.00359458
AFFX-BioB-M_at 487.292 P 0.000340305
AFFX-BioB-3_at 273.009 P 0.000169227
AFFX-BioC-5_at 790.824 P 0.000340305
AFFX-BioC-3_at 408.403 P 0.000169227
AFFX-BioDn-5_at 648.121 P 5.16732e-05
AFFX-BioDn-3_at 4633.39 P 0.000195116
AFFX-CreX-5_at 8601.84 P 4.42873e-05
AFFX-CreX-3_at 14112.4 P 4.42873e-05
AFFX-DapX-5_at 353.898 P 6.02111e-05
AFFX-DapX-M_at 643.324 P 0.00110197
AFFX-DapX-3_at 676.027 P 9.4506e-05
AFFX-LysX-5_at 48.3869 P 0.0396608
AFFX-LysX-M_at 116.705 A 0.425962
AFFX-LysX-3_at 137.265 P 0.000581214
AFFX-PheX-5_at 108.787 M 0.0629293
AFFX-PheX-M_at 61.6058 A 0.39692
AFFX-PheX-3_at 147.096 A 0.102165
AFFX-ThrX-5_at 100.288 A 0.205732
AFFX-ThrX-M_at 153.726 P 0.0103167

Total number of rows: 22769

Table truncated, full table size 867 Kbytes.




Supplementary file Size Download File type/resource
GSM219172.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM219172.CHP.gz 2.6 Mb (ftp)(http) CHP
GSM219172.EXP.gz 510 b (ftp)(http) EXP
Processed data included within Sample table
Processed data provided as supplementary file

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